The tests revealed that balls used at six stadiums on March 29 were livelier than they should have been.
Nippon Professional Baseball Commissioner Katsuhiko Kumazaki says "I want to apologize for causing a commotion."
Japanese baseball plans to re-test the ball and has asked ball manufacturer Mizuno to explain why the balls are livelier than what the league specified.
The apology is reminiscent of a ball controversy that hit Japanese baseball last season. Ryozo Kato, the previous commissioner, resigned in October to take responsibility after the official ball had been made livelier without his knowing. The juiced-up ball resulted in a dramatic increase in the number of home runs.